NEWS
fRagmentomics 0.99.12 (2026-03-31)
Pre-release version on Bioconductor devel.
fRagmentomics 0.99.11 (2026-03-10)
OTHER CHANGES
- Bioconductor compliance:
run_fRagmentomics() now returns a S4Vectors::DataFrame instead of a base data.frame.
- VCF import: Replaced the custom VCF parser with
VariantAnnotation::readVcf() for standard-compliant VCF reading. Compressed files (.vcf.gz) must now be bgzip-compressed and tabix-indexed. Added VariantAnnotation as an explicit dependency.
- Performance: Replaced incremental
rbind()/rbindlist() patterns in run_fRagmentomics(), normalize_mut(), and remove_bad_mut() with list-based collection followed by a single bind.
- Pipe cleanup: Replaced all
magrittr pipes (%>%) with the native R base pipe (|>) across all plotting functions. magrittr is no longer a dependency.
fRagmentomics 0.99.10 (2026-02-22)
OTHER CHANGES
- Windows Compatibility: Enforced strict LF line endings for FASTA files via
.gitattributes to prevent Rsamtools indexing errors (.fai) on Windows environments.
- Compatibility: Replaced native R pipes (
|>) with magrittr pipes (%>%) to ensure broader backward compatibility and avoid R (>= 4.1.0) dependency warnings.
fRagmentomics 0.99.9 (2026-02-18)
OTHER CHANGES
- Preparing pre-release version.
- Test: Add test to the package.
fRagmentomics 0.99.4 (2026-02-17)
NEW FEATURES
- Example Dataset: Added a benchmark case study featuring a 15-bp in-frame deletion in EGFR exon 19 (lung cancer cfDNA) to demonstrate indel-specific fragment sizing and genotyping.
- Reproducibility Scripts: Included data generation and anonymization scripts for the test dataset in
inst/scripts/.
- Developer Tools: Added a pre-commit configuration to standardize the development workflow.
OTHER CHANGES
- Documentation:
- Updated README and vignette to incorporate the new case study and illustrative figures.
- Testing: Updated the test suite to include coverage for the new EGFR case study.
fRagmentomics 0.99.3 (2026-02-16)
OTHER CHANGES
- QC Logic: Improved
process_fragment_reads_QC with updated default parameters and enhanced messaging for failed fragments.
- Code Refactoring: Factorized internal code and replaced
stop() calls in extract_fragment_features to improve robustness.
fRagmentomics 0.99.2 (2025-10-28)
OTHER CHANGES
- Improved
future.apply::future_lapply parallelization by setting properly the chunk parameter and reduced exported objects per worker.
fRagmentomics 0.99.1 (2025-10-22)
NEW FEATURES
- Added
flag_bam_list instead of TLEN (default: FALSE). Parameter to include all BAM fields in the output.
- Added
Position_3p to the output. Position_3p represents the last aligned position of the 3′ read of the fragment.
- Replaced rbind in the main function with
data.table::rbindlist to make it more consistent and faster.
OTHER CHANGES
- Change
future.apply::future_lapply parameter to remove a warning.
fRagmentomics 0.99.0 (2025-10-09)
NEW FEATURES
- Added
verbose (default FALSE) parameter to remove messages.
fRagmentomics 0.2.9 (2025-10-07)
NEW FEATURES
- Change fragment if DIS with potentially compatible with DIS.
OTHER CHANGES
- Update vignette.
- Fix some display errors on graph functions.
fRagmentomics 0.2.8 (2025-08-27)
NEW FEATURES
- Added new plotting functions for in-depth fragment analysis:
plot_size_distribution() to visualize fragment size distributions.plot_freq_barplot() to display nucleotide frequencies in end motifs.plot_ggseqlogo_meme() for generating sequence logo plots of end motifs using ggseqlogo.plot_motif_barplot() for generating end motifs in barplot.
OTHER CHANGES
- The package has been updated to meet all Bioconductor submission requirements.
fRagmentomics 0.2.7 (2025-08-15)
IMPROVEMENTS
- Improved fragment size calculation to more accurately account for insertions and deletions within the overlapping section of read pairs.
- Added the
remove_softclip parameter to trim soft-clipped bases from the ends of fragments.
fRagmentomics 0.2.6 (2025-07-30)
IMPROVEMENTS
- Upgraded BAM flag selection for more precise read filtering.
- Fragments with reads aligned in the same orientation are now automatically removed.
- The definition of 5' and 3' reads is now based on strand information rather than genomic position for greater accuracy.
fRagmentomics 0.2.5 (2025-07-10)
NEW FEATURES
- Introduced parallel processing (
future) and a progress bar (progressr) to significantly speed up analysis on multi-core systems.
IMPROVEMENTS
- Improved mutation classification for reads with soft-clipping at their ends, preventing potential false negatives. Cases previously classified as
WT are now correctly labeled AMB.
- Added an
Input_Mutation column to the output to retain the original mutation information before normalization.
fRagmentomics 0.2.4 (2025-06-25)
BUG FIXES
- Fixed a critical bug related to incorrect fetching of the reference sequence.
- Improved handling of ambiguous cases and multi-nucleotide variants (MNVs).
- Optimized the SNV detection algorithm.
fRagmentomics 0.2.3 (2025-06-12)
IMPROVEMENTS
- Improved performance by replacing per-fragment FASTA requests with a single, larger request per mutation, resulting in a 1.5x to 2x speed increase.
fRagmentomics 0.2.2 (2025-05-20)
IMPROVEMENTS
- Introduced more descriptive mutation statuses (e.g.,
"MUT but potentially larger MNV", "OTH (DEL)").
- Updated the reporting of
BASE_5p and BASE_3p to be more comprehensive around the variant position.
- Finalized the definitions for
Fragment_Status_Simple and Fragment_Status_Detail columns.
BUG FIXES
- Corrected mutation status assignment for reads with hard or soft-clipping near the variant.
- The
get_index_aligning_with_pos() function now correctly handles deletions at the position of interest.
OTHER CHANGES
- Renamed parameter
cigar_free_mode to cigar_free_indel_match for clarity.
fRagmentomics 0.2.1 (2025-05-01)
BUG FIXES
- Corrected the Variant Allele Frequency (VAF) calculation.
OTHER CHANGES
- Harmonized all output column names to use "Upper_Snake_Case" for consistency.
fRagmentomics 0.2.0 (2025-04-15)
NEW FEATURES
- Implemented a new, alternative algorithm for determining mutation status that is independent of the CIGAR string. This significantly improves INDEL detection and is controllable via the
cigar_free_indel_match parameter.
OTHER CHANGES
- Major code refactoring for clearer function names and better maintainability.
fRagmentomics 0.1.0 (2025-03-01)
NEW FEATURES
- Initial beta version of the package.
- Core functionality for extracting key fragmentomic features, including end motifs and fragment size.
- Initial implementation of fragment mutational status classification (e.g.,
WT, MUT, AMB, and more complex states)